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It is all about the sound. If you are playing one chord and you change to a different chord for example C Major to F Major.
You want to move the tones as few notes as possible to get the new chord.
So if your C chord is in root inversion ( CEG from lowest to highest) then the most logical F chord is CFA from lowest to highest or second inversion. This is because the C is common to both and E to F is just 1 half step ( the smallest possible movement in our scale system) G to A is a Whole step (the second smallest possible movement in our scale system).
This is going to sound much better than moving the whole chord to F in root position ( Either up 7 half steps or down 5 half steps)

This process is called voice leading, and is essential to making Vocal harmonies sound good ( and capable of being sung!)

I suggest you try this idea out on some of your favorite chord changes.

The rules:
Look for common tones then move the rest of the notes as short a distance as possible.
The exception is when moving from IV to V or ii to iii because this would give you parallel movement. This would be best handled by inverting one of the two chords.